[Neuroimaging] [DIPY] Question about whole tracks *.trk registration using SLR

[Eleftherios Garyfallidis]

Hi Rodrigo,

Apologies for the delay. But hey I got a solution for you! I hope you are
excited :)
Look at this gist
https://gist.github.com/Garyfallidis/51e34aab47de99eafa887b2b818384ea

This code shows how to do step by step whole brain SLR and I made it work
with the
specific datasets that you gave me.

The specific datasets don't need exactly a whole brain SLR because the one
brain has much
fewer structures than the other brain but still SLR is robust to incomplete
datasets such as these.

Give it a go and give us feedback! :)

All the best,
Eleftherios

p.s. Notice that to load the streamlines I used a more recent API than what
you originally used. Make sure you have a recent version of dipy and
nibabel.


On Mon, Sep 25, 2017 at 9:50 AM Perea Camargo, Rodrigo Dennis <
RPEREACAMARGO at mgh.harvard.edu> wrote:

> Hi Eleftherios,
> I am included both *.trk files in here:
> http://www.nmr.mgh.harvard.edu/~rdp20/drop/trk_slf/
> IIT2mean.trk was a template TRK downloaded from the tract_querier example (
> http://tract-querier.readthedocs.io/en/latest/ ) and
> ADRC_TMP_wholeBrain.trk.gz was generated using dsi_studio (
> http://dsi-studio.labsolver.org/)
>
> Thanks again,
>
> Rodrigo
>
>
>
> On Sep 21, 2017, at 3:46 PM, Eleftherios Garyfallidis <elef at indiana.edu>
> wrote:
>
> Hi Rodrigo,
>
> Whole brain SLR is a great idea! Thank you for your question.  :)
>
> Have in mind that nibabel.trackvis is the old API. Use
> nibabel.streamlines.load instead.
>
> Can you please share with me (off the list) your trk files so that I can
> correct your
> script?
>
> A wild guess is that you are not loading the streamlines correctly.
>
> Did you use DIPY to create those trks or another software?
>
> Also, another suggestion is to run QuickBundles first to reduce the size
> of your
> datasets. I mean before starting the SLR.
>
> Here is a sample script (in one of my branches).
>
> https://github.com/Garyfallidis/dipy/blob/recobundles/dipy/workflows/align.py
>
> We are working on making something similar available asap in master.
>
> Best,
> Eleftherios
>
>
>
> On Thu, Sep 21, 2017 at 1:36 AM Perea Camargo, Rodrigo Dennis <
> RPEREACAMARGO at mgh.harvard.edu> wrote:
>
> Hi Eleftherios & DIPY community,
>> I am trying to register two whole brain tracts as shown in your recent
>> publication using the streamline-based linear registration. I am diving
>> into Dipy now and I might have some problems loading the files or
>> registering them.
>> Following your example (
>> http://nipy.org/dipy/examples_built/bundle_registration.html#example-bundle-registration),
>> there are 2 issues that may arise when I try it.
>>
>> 1) How to load *.trk files is not shown in your example (it looks like
>> you added to cingulum bundles from your dataset using the dipy.data value…)
>> So I follow this tutorial (
>> http://nipy.org/dipy/examples_built/streamline_formats.html ) to load
>> the streamline and hdr but I am not sure if this is the format SLF() wants
>> it in.
>>
>> 2) So then I try using the srr.optimize( ) function but I get the
>> following problems (check below).
>>
>> I hope you can help me.
>> Rodrigo
>>
>>
>> Here is my Jupyter notebook with the errors I found (any help will be
>> greatly appreciate it):
>>
>>
>>
>>
>>
>>
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